So
Here's a theory:
The revolution won... Everything was fine... For about thirty seconds.
Seeing as Freeman didn't exist in this timeline, this is what WOULD have happened in the events of Half Life 2/episode 1+2 without his intervention.
The G-Man sees all this, and sees how Earth ends, effectively, and finds a convergence point (Where two or more alternate Universes meet) where he can insert Gordon Freeman back into the timeline to kick start it all again, without destroying space-time.
Hence "Insert Subject Freeman".
So...
My theory is that Helix is gonna be Half Life RP but with Gordon Freeman in it or involved at least AT SOME POINT in the story... And that this will be more similar in some way to the actual Half Life 2 story, but with the Nebulous Cloud lore twists.